December 28, 2012

FTDNA draft Y-chromosome phylogeny

A draft of the Y-chromosome phylogeny, including the newly discovered basal A00 clade has been posted by FTDNA. Hopefully some progress can be made in the F portion of the tree, where currently there are subclades F1,F2,F3,G,H, and IJK. Determination of the bifurcation structure within F will doubtlessly be instrumental in informing our understanding of the dispersal of F descendants, which, according to the age of this major Eurasian haplogroup, are closely linked to the Upper Paleolithic event in Eurasia.

Investing in whole-genome sequencing of one individual from each of these clades would be very helpful in determining this structure. Of course, there are already the Complete Genomics data which include haplogroup G and various IJK descendants, so we now need to identify some F1,F2,F3, and H samples and give them the WGS treatment.

11 comments:

I personally identified these haplotypes, raised the money for the testing, and paid for testing them myself.There was a deliberate attempt to zero out payments after the orders were placed. However, in spite of their efforts, not all payments were zeroed out.

The Genographic Project and FTDNA commercialized SNPs without permission and expressly against the wishes of the donor of the sample who required that all the people who paid be notified officially and formally of the results before any publication of the results. This condition was not met.

This was never intended to be commercialized. FTDNA, Thomas Krahn, and the Genographic Project steadfastly refused to test these samples themselves. The quote from Bennett Greenspan when I asked about finding precisely such haplotypes was "case closed."

What FTDNA and the Genographic Project did was allow paying customers interested in science to "prospect" for SNP and then when those customers find something, they "jump the claim" to say that they have the right to commercialize it.

FTDNA had a commercial obligation not only to adhere to their "SNP Assurance Program" guarantee of a placement on the Y tree for "FREE" (quote) but also to report all Y SNPs to the Y Chromosome Consortium members for publication.

Charges have been filed in this case. FTDNA has already been notified of this.

And for those who are interested in science, not politics or commercialization of DNA results by private companies, here is an in Build 37 that I converted from Build 36, edited and verified myself:Y SNPs & PGP 1-50 & CGI 1-69

I notice that the PF (Paolo Francalacci) SNPs are listed, but not the "CTS" (Chris Tyler-Smith) SNPs. Chris Tyler-Smith recieved a grant from the Wellcome Trust to do whole genome sequencing for world populations for the 1000 Genomes Project. That put his group at the Sanger Institute under obligation to submit these SNPs publicly to Genbank. At the same time, the same people were working for the Genographic Project which was creating a commercial chip as a product which had SNPs from the 1000 Genomes Project that were withheld from the Y Chromosome Consortium and Genbank. SNPs were put on this chip that were paid for by customers of FTDNA not only without their express permission, but also after explicit business promises by Bennett Greenspan that they would not be commercialized. Unethical, a violation, and likely illegal (which is for the appropriate law enforcement agencies to decide). The clear evidence of the commercialization of SNP results without the required reporting is right here. Furthermore, this calls into question forensic Y testing, because SNPs that were critical for identifying males (due to the failure of the Y Amelogenin test) were withheld from forensic use and from law enforcement authorities. The implications of these actions go far beyond mere Y ancestry.

Again, for those that are interested in doing their own investigation of the Y, the UCSC Browser Track I created comparing the new Y SNPs with the PGP and Complete Genomics Y sequences:

COMMENTS(12):"Hmm...I am also a former HOGL employee and have to say that my experience was very negative. I question the merit of the projects. No one seems that interested in the projects other than their own advancements and in my field, that is not science, that's just making money. I also found the work environment to be extremely unprofessional, even bordering on illegal. Having been on the inside, I was aware of many things that took place outside of the work environment and if you were not part of it, you were not welcome there.I don't know where all of these other comments came from but how coincidental that they all are written in a very short period of time. Almost like some sort of propaganda mission. HOGL's activities benefit only HOGL and it's employees. That was the worst time at the University I ever spent.By the way, the first comment posted was a pretty accurate account of what the real priorities of HOGL are. Why was it taken down? TW should be ashamed in helping to cover up the truth!

Dienekes, I just wanted to say, if you're referring to Thomas' latest draft tree, that is not by any means the new, official FTDNA / Genographic phylogeny. It is just what it's always been, Thomas Krahn's personal working tree. The great majority of the Genographic SNPs aren't on it yet. We are still waiting for Genographic, not Thomas, to release their phylogeny, hopefully in the coming weeks.

It's hard not to be provoked by the falsehoods Ted is promulgating. I hope people who aren't directly involved will not let themselves be fooled by someone who is unfortunately suffering from a mental illness. I know my colleagues won't want to be dragged down into arguing with Ted, but I don't appreciate seeing them falsely accused, which leads me to speak up. I don't want to make Ted's rants seem worthy of serious debate, but sometimes, if you don't step forward to state the real facts, there are people who will suppose that these kinds of accusations could have some truth to them. I'm not going to go back and forth, arguing on and on with Ted, but I'll post a few key facts.

Ted contributed a *tiny* amount of money, and tried to raise funds, with very little effect; he was in no way responsible for our being able to conduct the research on A00. Our very generous friend Stan, and his friends in Poland, did indeed make our research possible, by contributing by far the largest portion, and another friend in Mexico contributed a lot to get us off the ground in the early months of the project. I would credit them by name except that I don't know whether they wish to be named here. If they do wish to speak up themselves, they'll corroborate what I'm saying.

Any impression one might get from his statements that any of the SNPs from the family Ted is referring to were used on the Genographic chip is completely false. If he thinks they were, Ted simply doesn't know what he is talking about. If he looked at even one set of Geno 2.0 test results, he could see that neither the A00 SNPs nor the A0 SNPs are included on the chip (the highest-numbered L-SNP on it is L808). The cut-off date for SNPs to go onto the chip was in November of 2011, long before the A00 SNPs were discovered in 2012.

The family in question fully supports all the findings from the research being published. These SNPs' details have now been published online in Ytree and Ymap, so of course they are available for any company in the world to incorporate into their genetic testing products, just like any other SNP; there's nothing that would put these positions on the Y chromosomes off-limits. FTDNA and Genographic won't keep any secret, proprietary knowledge about them. If any other company wants to -- if they cared enough about Y-DNA testing -- they're perfectly free to offer to test them, like any other part of the genome.

It's ludicrous that Ted accuses a business of making a profit as though that were a violation of legal or moral codes. . . FTDNA is not a non-profit or educational organization, they are a business, which cannot operate without making some profit. They're not accumulating any vast wealth, that's for sure. Most of us think they are by far the most conscientious and sincerely customer-oriented business in the field of genetic ancestry testing. Not that I agree with them on everything, but who do you prefer? Ancestry.com? 23andMe? Good luck doing any research on the Y chromosome with them!

Dienekes, agreed. This is not the forum for that sort of thing. However, the issue at hand is the Y phylogeny and how it relates to this "announcement".

My main complaint over many years (and I have much written evidence to back this up) is that the Y phylogeny, critical for forensic identification as well as human origins and genealogy, was being ignored, or rather commercialized for reasons that had nothing to do with science. This update in fact is provably incomplete.

Z489 as well as the Z478 Z487 Z493 SNPs are known to be precisely under L210 and L227 etc. Z489 was "discovered" in the 1K Genomes by "BES" last year, reported to Thomas Krahn - but not to the YCC - and was not put on the ISOGG tree, yet was made available for testing by FTDNA. (That's how it was discovered.)

The Ashkenazi cluster is Z489+ Z478- Z487- Z493- and the TSI Tucscans are derived for all 4 SNPs. The Ashkenazi cluster includes some extremely well-known families who also happen to have pedigrees going back to the 16th century, as well as perhaps one or two Calabrians/Sicilians.

Why were these SNPs left off the Y phylogeny, even though they were present in the 1K Genomes raw data, and were available and promoted as tests on the FTDNA site? I have an idea, but I won't say it and in fact any excuse is irrelevant.

Solution:We need to have a Y phylogenetic tree that:1. Is under the control of a neutral, non-profit forensically based entity (I can think of appropriate neutral parties I would support that are not part of an organization that I belong to, but I would be happy to help facilitate)2. This group should not have a conflict of interest in any way, either commercial or as part of a group of customers "beholden" to one or more commercial testing companies3. Be continually updated in an open participatory way by as large a number of people as possible4. All Y SNPs need to be reported to the only repository of SNPs agree upon by the entire world, NCBI Genbank dbSNP. If verified, these SNPs need to be reported as soon as possible (and not "saved up in a batch').

People who say that they are "Genetic Genealogists" forget that the Y phylogeny is in fact a matter of life or death. It is used for identification of rapists (remember, only men have a Y), the remains of unidentified missing males, and could be used by the families of missing males to help screen others (remains and living persons) for identification. It's of psychological and medical importance for adoptees. Most important, the Y can be used to free the wrongly convicted, and perhaps even prevent the execution of an innocent person. Hence, the Y phylogeny, especially with "private" SNPs which are useful for precise identification needs to be considered on a much broader humanistic basis than now.

As I said, I have a practical solution for this and I have been and am willing to contribute my own money toward making this happen (by buying server space).

Remember, that "hidden SNP" may in fact be the difference between the conviction and execution of an innocent person and the identification of an at-large perpetrator.

If people think that this does not happen, think ""Central Park Jogger Case". We who are interested in the science of the Y and human origins have an ethical responsibility to make sure that this is done right for many reasons, not just basic scientific understanding, but social justice toward native peoples, understanding the sources of shared ancestry around the world (e.g. "Ashkenazi" Y clades among tens of thousands of Hispanics), psychological peace for adoptees, the families of missing persons, and crime victims, and freeing the innocent.

LOL, yeah, life and death, right! If our national security infrastructure had to rely on ISOGG..!

Reasons many SNPs in A and J take forever to show up on ISOGG tree:1. I work full time for a living2. My health isn't great, lack of sleep, exhaustion3. No partner to share work, responsibilities, bills4. House full of cats to take care of5. Overwhelmed with emails, project management6. Huge amounts of data to analyze etc.

I have used the FTDNA draft Y-Chromosome Phylogeny and I have found it to be generally quite useful, especially the feature where you can click on an SNP and you can find out its position on the Y-Chromosome (for Build 36) and other detailed information on it. However, there are some cases it is not in-sync with all other publications, and/or findings that may come outside of the FTDNA eco-system, for instance take the SNP E-V92, a subclade of E-M35 that was published in January of 2011, this SNP still has not made it into the FTDNA draft tree, however E-V68, that was published at the same time, has made it into the tree, therefore, I caution cross-referencing with other publications or even ISOGG to get the most current picture, although ISOGG can have its own drawbacks as well, like being late for instance.

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